I use tmdb episode ordering for this show and they match correctly once you name the files correctly. The Heart of Archness
episodes are considered specials, see the link for details → Archer: Season 0 — The Movie Database (TMDB)
So, Archer - S00E03
, Archer - S00E04
and Archer - S00E05
would be how you name those episodes.
Looking at tvdb does the same Archer (2009) - Aired Order - Specials - TheTVDB.com
You may need to plex dance the show if you have manually done edits.